1. D.M. Ozata, I. Gainetdinov, A. Zoch, D. O'Carroll, P.D. Zamore.
PIWI-interacting RNAs: small RNAs with big functions. Nat.
Rev. Genet. 20, 89–108 (2019). doi: 10.1038/s41576-018-0073-3
pmid: 30446728
2. Y.W. Iwasaki, M.C. Siomi, H. Siomi. Piwi-interacting RNA: Its
biogenesis and functions. Annu. Rev. Biochem. 84, 405–433
(2015). doi: 10.1146/annurev-biochem-060614-034258 pmid:
25747396
3. H.
Yamashiro,
M.C.
Siomi.
PIWI-interacting
RNA
in
Drosophila: Biogenesis, transposon regulation, and beyond.
Chem
Rev.
118,
4404–4421
(2018).
doi:
10.1021/acs.chemrev.7b00393 pmid: 29281264
4. B. Czech, G.J. Hannon. One loop to rule them all: the
ping-pong cycle and piRNA-guided silencing. Trends Biochem.
Sci. 41, 324–337 (2016). doi: 10.1016/j.tibspmid: 26810602
128
5. T. Schüpbach, E. Wieschaus. Female sterile mutations on the
second chromosome of Drosophila melanogaster. II. Mutations
blocking oogenesis or altering egg morphology. Genetics 129,
1119–1136 (1991). pmid: 1783295
6. C. Klattenhoff, D.P. Bratu, N. McGinnis-Schultz, B.S.
Koppetsch, H.A.Cook, W.E. Theurkauf. Drosophila rasiRNA
pathway mutations disrupt embryonic axis specification
through activation of an ATR/Chk2 DNA damage response.
Dev. Cell 12, 45–55 (2007). doi:10.1016/j.devcel.2006.12.001
pmid: 17199040
7.
A.A. Aravin, N.M. Naumova, A.V.Tulin, V.V. Vagin,
Y.M.Rozovsky, V.A.Gvozdev. Double-stranded RNA-mediated
silencing of genomic tandem repeats and transposable
elements in the D. melanogaster germline. Curr Biol.
11,1017-27 (2001). pmid: 11470406
8. V.V. Vagin, A. Sigova, C. Li, H. Seitz, V. Gvozdev, P.D.
Zamore. A distinct small RNA pathway silences selfish genetic
elements in the germline. Science 313, 320–324(2006). doi:
10.1126/science.1129333 pmid: 16809489
129
9. J. Brennecke, A.A. Aravin, A. Stark, M. Dus, M. Kellis, R.
Sachidanandam, G.J. Hannon. Discrete small RNA-generating
loci as master regulators of transposon activity in Drosophila.
Cell. 128, 1089–1103(2007). doi:
10.1016/j.cell.2007.01.043
pmid: 17346786
10.
L.S. Gunawardane, K. Saito, K.M. Nishida, K. Miyoshi, Y.
Kawamura,
T.
Nagami,
H.
Siomi,
M.C.
Siomi.
slicer-mediated mechanism for repeat-associated siRNA 5’ end
formation in Drosophila. Science 315, 1587-1590 (2007).
doi:10.1126/science.1140494 pmid: 17322028
11.
K. Saito, H. Ishizu, M. Komai, H. Kotani, Y. Kawamura,
K.M. Nishida, H. Siomi, M.C. Siomi. Roles for the Yb body
components Armitage and Yb in primary piRNA biogenesis in
Drosophila.
Genes
Dev.
24,
2493–2498
(2010).
doi:
10.1101/gad.1989510 pmid: 20966047
12.
G. Sienski, D. Dönertas, J. Brennecke. Transcriptional
silencing of transposons by Piwi and maelstrom and its impact
130
on chromatin state and gene expression. Cell 151, 964–980
(2012). doi: 10.1016/j.cell.2012.10.040 pmid: 23159368
13.
N.V. Rozhkov, M. Hammell, G.J. Hannon. Multiple roles
for Piwi in silencing Drosophila transposons. Genes Dev. 27,
400–412(2013). doi: 10.1101/gad.209767.112 pmid: 23392609
14.
A. Le Thomas, A.K. Rogers, A. Webster, G.K .Marinov, S.E.
Liao, E.M. Perkins, J.K. Hur, A.A. Aravin, K.F. Toth. Piwi
induces
piRNA-guided
transcriptional
silencing
and
establishment of a repressive chromatin state. Genes Dev. 27,
390–399
15.
(2013). doi: 10.1101/gad.209841.112 pmid: 23392610
M.S. Klenov, S.A. Lavrov, A.P. Korbut, A.D. Stolyarenko,
E.Y. Yakushev, M. Reuter, R.S. Pillai, V.A. Gvozdev. Impact of
nuclear Piwi elimination on chromatin state in Drosophila
melanogaster ovaries. Nucleic Acids Res. 42, 6208–6218 (2014).
doi: 10.1093/nar/gku268 pmid: 24782529
16.
S. Hirakata, H. Ishizu, A. Fujita, Y. Tomoe, M.C. Siomi.
Requirements for multivalent Yb body assembly in transposon
131
silencing in Drosophila. EMBO Rep. e47708 (2019). doi:
10.15252/embr.201947708 pmd: 31267711
17.
H. Nishimasu, H. Ishizu, K. Saito, S. Fukuhara, M.K.
Kamatani, L. Bonnefond, N. Matsumoto, T. Nishizawa, K.
Nakanaga, J. Aoki, R. Ishitani, H. Siomi, M.C. Siomi, O.
Nureki. Structure and function of Zucchini endoribonuclease in
piRNA
biogenesis.
Nature
491,
284-7
(2019).
doi:
10.1038/nature11509 pmid: 23064230
18.
D. Handler, K. Meixner, M. Pizka, K. Lauss, C. Schmied,
F.S. Gruber, J. Brennecke. The genetic makeup of the
Drosophila piRNA pathway.
(2013)
doi:
Mol. Cell 50, 762-777
pmid:10.1016/j.molcel.2013.04.031
pmid:
23665231
19.
B. Czech, J.B. Preall, J. McGinn, G.J. Hannon. A
transcriptome-wide RNAi screen in the Drosophila ovary
reveals factors of the germline piRNA pathway. Mol. Cell
50,749-61 (2013). doi: 10.1016/j.molcel.2013.04.007 pmid:
23665227
132
20.
K. Saito, S. Inagaki, T. Mituyama, Y. Kawamura, Y. Ono,
E. Sakota, H. Kotani, K. Asai, H. Siomi, M.C. Siomi. A
regulatory circuit for piwi by the large Maf gene traffic jam in
Drosophila.
Nature
461,
1296–1299
(2009).
doi:
10.1038/nature08501 pmid:19812547
21.
H. Yamashiro, M. Negishi, T. Kinoshita, H. Ishizu, H.
Ohtani, and M.C. Siomi. Armitage determines
Piwi-piRISC processing from precursor formation and quality
control to inter-organelle translocation. EMBO Rep. e48769
(2020) doi: 10.15252/embr.201948769
22.
G.J.
Y. Yu, J. Gu, Y. Jin, Y. Luo, J.B. Preall, J. Ma, B. Czech,
Hannon.
Panoramix
enforces
piRNA-dependent
cotranscriptional silencing. Science 350, 339–342 (2015). doi:
10.1126/science.aab0700 pmid: 26472911
23.
G. Sienski, J. Batki, K.A. Senti, D. Dönertas, L. Tirian, K.
Meixner,
J.
Piwi-piRNA
machinery.
Brennecke.
complex
Genes
Silencio/CG9754
connects
to
the
cellular
Dev.
29,
2258–2271
10.1101/gad.271908.115 pmid: 26494711
133
the
heterochromatin
(2015).
doi:
24.
D. Dönertas, G. Sienski, J. Brennecke. Drosophila Gtsf1 is
an essential component of the Piwi-mediated transcriptional
silencing complex. Genes Dev. 27, 1693–1705 (2013). doi:
10.1101/gad.221150.113 pmid: 23913922
25.
H. Ohtani, Y.W. Iwasaki, A. Shibuya, H. Siomi. M.C.
Siomi,
K.
Saito.
DmGTSF1
is
necessary
for
Piwi-piRISC-mediated transcriptional transposon silencing in
the Drosophila ovary. Genes Dev. 27, 1656–1661 (2013). doi:
10.1101/gad.221515.113 pmid: 23913921
26.
Y.W. Iwasaki, K. Murano, H. Ishizu, A. Shibuya, Y. Iyoda,
M.C. Siomi, H. Siomi, K. Saito. Piwi modulates chromatin
accessibility by regulating multiple factors including histone
H1 to repress transposons. Mol. Cell 63, 408–419 (2016). doi:
10.1016/j.molcel.2016.06.008pmid:27425411 pmid: 2742541
27.
X.A. Huang, H. Yin, S. Sweeney, D. Raha, M. Snyder, H.
Lin. A major epigenetic programming mechanism guided by
piRNAs.
Dev.
Cell
24,
502–516
10.1016/j.devcel.2013.01.023 pmid: 23434410
134
(2013).
doi:
28.
M.H. Fabry, F. Ciabrelli, M. Munafò, E.L. Eastwood, E.
Kneuss, I. Falciatori, F.A. Falconio, G.J. Hannon, B. Czech.
piRNA-guided co-transcriptional silencing coopts nuclear
export factors. eLife e47999 (2019). doi: 10.7554/eLife.47999
pmid: 31219034
29.
K. Murano, Y.W. Iwasaki, H. Ishizu, A. Mashiko, A.
Shibuya, S. Kondo, S. Adachi, S. Suzuki, K. Saito, T. Natsume,
M.C. Siomi, H. Siomi. Nuclear RNA export factor variant
initiates piRNA-guided co-transcriptional silencing. EMBO J.
e102870
(2019).
doi:
10.15252/embj.2019102870
pmid:
31368590
30.
C.E.
J. Batki, J. Schnabl, J. Wang, D. Handler, V.I. Andreev,
Stieger,
M.
Novatchkova,
L.
Lampersberger,
K.
Kauneckaite, W. Xie, K. Mechtler, D.J. Patel, J. Brennecke.
The
nascent
RNA
binding
complex
SFiNX
licenses
piRNA-guided heterochromatin formation. Nat. Struct. Mol.
Biol. 26: 720–731 (2019). doi: 10.1038/s41594-019-0270-6 pmid:
31384064
135
31.
K. Zhao, S. Cheng, N. Miao, P. Xu, X. Lu, M. Wang, Y.
Zhang, X. Yuan, W. Liu, X. Lu, X. Ouyang, P. Zhou, J. Gu, Y.
Zhang, D. Qiu, S. Wang, Z. Jin, Y. Wan, J. Ma, H. Cheng, Y.
Huang, Y. Yu. A Pandas complex adapted for piRNA-guided
transposon silencing. Nat Cell Biol. 21, 1261-1272 (2019). doi:
https://doi.org/10.1101/608273
32.
K. Ohsumi, K. Sato, K. Murano, H. Siomi, M.C. Siomi.
Essential roles of Windei and nuclear monoubiquitination of
Eggless/SETDB1 in transposon silencing. EMBO Rep. e48296
(2019). doi: 10.15252/embr.201948296 pmid: 31576653
33.
D.
Holoch,
D.
Moazed.
RNA-mediated
epigenetic
regulation of gene expression. Nat Rev Genet. 16,71-84 (2015).
doi: 10.1038/nrg3863 pmid: 25554358
34.
N. J. Clegg, D. M. Frost, M. K. Larkin, L. Subrahmanyan,
Z. Bryant, H. Ruohola-Baker. maelstrom is required for an
early step in the establishment of Drosophila oocyte polarity:
posterior localization of grk mRNA. Development 124,4661
-4671 (1997).
136
35.
T.H. Chang, E. Mattei, I. Gainetdinov, C. Colpan, Z. Weng,
P.D. Zamore. Maelstrom Represses Canonical Polymerase II
Transcription
within
Bi-directional
piRNA
Clusters
in
Drosophila melanogaster. Mol. Cell 73, 291-303 (2019). doi:
10.1016/j.molcel.2018.10.038 pmid: 30527661
36.
C.W.
Roberts,
S.H.
Orkin.
The
SWI/SNF
complex--chromatin and cancer. Nat. Rev. Cancer 4, 133-42
(2004). doi: 10.1038/nrc1273 pmid: 14964309
37.
J.A. Kennison, J.W. Tamkun. Dosage-dependent modifiers
of Polycomb and Antennapedia mutations in Drosophila. Pros.
Natl. Acad. Sci. 85, 8136–8140 (1988). pmid:3141923
38.
J.W. Tamkun, R. Deuring, M.P. Scott, M. Kissinger, A.M.
Pattatucci, T.C. Kaufman, J.A. Kennison. Brahma: a regulator
of Drosophila homeotic genes structurally related to the yeast
transcriptional activator SNF2/SWI2. Cell 68, 561–572 (1992).
pmid:1346755
39.
O. Papoulas, S.J. Beek, S.L. Moseley, C.M. McCallum, M.
Sarte, A. Shearn, J.W. Tamkun. The Drosophila trithorax
137
group proteins BRM, ASH1 and ASH2 are subunits of distinct
protein complexes. Development 125, 3955–3966 (1998).
pmid:9735357
40.
R.T. Collins, T. Furukawa, N. Tanese, J.E. Treisman. Osa
associates with the Brahma chromatin remodeling complex
and promotes the activation of some target genes. EMBO J. 18,
7029–7040
(1999).
doi:
10.1093/emboj/18.24.7029
pmid:10601025
41.
A.J. Kal, T. Mahmoudi, N.B. Zak, C.P. Verrijzer. The
Drosophila Brahma complex is an essential coactivator for the
trithorax group protein Zeste. Genes Dev. 14, 1058–1071
(2000). pmid:10809665
42.
L. Mohrmann, K. Langenberg, J. Krijgsveld, A.J. Kal, A.J.
Heck C.P. Verrijzer. Differential targeting of two distinct
SWI/SNF-related Drosophila chromatin-remodeling complexes.
Mol. Cell Biol. 24, 3077–3088 (2004). pmid:15060132
43.
B.J. Brizuela, L. Elfring, J. Ballard, J.W. Tamkun, J.A.
Kennison. Genetic analysis of the brahma gene of Drosophila
138
melanogaster and polytene chromosome subdivisions 72AB.
Genetics 137, 803–813 (1994). pmid:7916308
44.
D. Handler, D. Olivieri, M. Novatchkova, F.S. Gruber, K.
Meixner, K. Mechtler, A. Stark, R. Sachidanandam, J.
Brennecke. A systematic analysis of Drosophila TUDOR
domain-containing proteins identifies Vreteno and the Tdrd12
family as essential primary piRNA pathway factors. EMBO J.
30, 977-93 (2011). doi: 10.1038/emboj.2011.308 pmid: 21863019
45.
H. Ishizu, Y.W. Iwasaki, S. Hirakata, H. Ozaki, W.
Iwasaki, H. Siomi, M.C. Siomi. Somatic primary piRNA
biogenesis driven by cis-acting RNA elements and trans-acting
Yb.
Cell
Rep.
12,
429–440
(2015).
doi:
10.1016/j.celrep.2015.06.035
46.
K. Saito, K.M. Nishida, T. Mori, Y. Kawamura, K. Miyoshi,
T. Nagami, H. Siomi, M.C. Siomi. Specific association of Piwi
with
rasiRNAs
derived
from
retrotransposon
and
heterochromatic regions in the Drosophila genome. Genes Dev.
20,
2214–2222
(2006).
doi:
16882972
139
10.1101/gad.1454806
pmid:
47.
K, Sato, K.M. Nishida, A. Shibuya, M.C. Siomi, H. Siomi.
Maelstrom
coordinates
microtubule
organization
during
Drosophila oogenesis through interaction with components of
the
MTOC.
Genes
Dev.
25,
2361–2373
(2011).
doi:
10.1101/gad.174110.111 pmid: 22085963
48.
T. Nakayama, T. Shimojima, S. Hirose. The PBAP
remodeling complex is required for histone H3.3 replacement
at
chromatin
boundaries
and
for
boundary
functions.
Development 139, 4582–4590 (2012). doi: 10.1242/dev.083246
pmid: 23136390
49.
G.S. Pall, A.J. Hamilton. Improved northern blot method
for enhanced detection of small RNA. Nat. Protoc. 3, 1077-84
(2008). doi: 10.1038/nprot.2008.67 pmid: 18536652
50.
B.W. Han, W. Wang, P.D. Zamore, Z. Weng. piPipes: a set
of pipelines for piRNA and transposon analysis via small
RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and
genomic DNA sequencing. Bioinformatics 31, 593–595 (2015).
doi: 10.1093/bioinformatics/btu647pmid: 25342065
140
51.
B. Mugat, S. Nicot, C. Varela-Chavez, C. Jourdan, K. Sato,
E. Basyuk, F. Juge, MC. Siomi, A. Pelisson, S. Chambeyron.
The Mi-2 nucleosome remodeler and the Rpd3 Histone
deacetylase are involved in piRNA-guided heterochromatin
formation.
Nat.
Commun.
11,
2818
(2020).
doi:
10.1038/s41467-020-16635-5
52.
M. Ninova, Y. A. Chen, B. Godneeva, A.K. Rogers, Y. Luo,
K. Fejes Tóth, A. A. Aravin. Su(var)2-10 and the SUMO
pathway link piRNA-guided target recognition to chromatin
silencing.
Mol.
Cell
77,
556–570
(2020).
doi:
10.1016/j.molcel.2019.11.012
53.
E. Sarot, G. Payen-Groschêne, A. Bucheton, A.E.
Pélisson Evidence for a piwi-dependent RNA silencing of the
gypsy endogenous retrovirus by the Drosophila melanogaster
flamenco
gene.
Genetics
166,
313–321
(2004).
doi:
10.1534/genetics.166.3.1313 pmid: 15082550
54.
A. Pélisson, G. Payen-Groschêne, C. Terzian, A. Bucheton.
Restrictive flamenco alleles are maintained in Drosophila
141
melanogaster population cages, despite the absence of their
endogenous gypsy retroviral targets. Mol. Biol. Evol. 24, 498–
504 (2007). doi: 10.1093/molbev/msl176 pmid: 17119009
55.
L.K. Elfring, l.C. Danie, O. Papoulas, R. Deuring, M. Sarte,
S. Moseley, S.J. Beek, W.R. Waldrip, G. Daubresse, A. DePace,
J.A. Kennison, J.W. Tamkun. Genetic analysis of brahma: The
Drosophila homolog of the yeast chromatin remodeling factor
SWI2/SNF2. Genetics 148, 251–265 (1998). pmid: 9475737
56.
J.A. Armstrong, O. Papoulas, G. Daubresse, A.S. Sperling,
J.T. Lis, M.P. Scott, J.W. Tamkun. The Drosophila BRM
complex facilitates global transcription by RNA polymerase II.
EMBO J. 21, 5245–5254 (2002). doi: 10.1093/emboj/cdf517
pmid: 12356740
57.
Y.M. Moshkin, L. Mohrmann, W.F. van Ijcken, C.P.
Verrijzer. Functional differentiation of SWI/SNF remodelers in
transcription and cell cycle control. Mol. Cell Biol. 27, 651–661
(2007). doi:10.1128/MCB.01257-06 pmid: 17101803
142
58.
A.K. Dingwall, S.J. Beek, C.M. McCallum, J.W. Tamkun,
G.V. Kalpana, S.P. Goff, M.P. Scott. The Drosophila snr1 and
brm proteins are related to yeast SWI/SNF proteins and are
components of a large protein complex. Mol. Biol. Cell 6, 77–
91(1995). pmid: 7579694
59.
J. Baron-Benhamou, N.H. Gehring, A.E. Kulozik, M.W.
Hentze. Using the lambdaN peptide to tether proteins to RNAs.
Methods in Mol. Biol. 257, 135–154 (2004).
doi:10.1385/1-59259-750-5:135 pmid: 14770003
60.
N. Matsumoto, K. Sato, H. Nishimasu, Y. Namba, K.
Miyakubi, N. Dohmae, R. Ishitani, H. Siomi, M.C. Siomi, O.
Nureki. Crystal structure and activity of the endoribonuclease
domain of the piRNA pathway factor Maelstrom. Cell Rep. 11,
366–375
(2015).
doi:
10.1016/j.celrep.2015.03.030
pmid:
25865890
61.
M.
C. Tréand, I. du Chéné, V. Brès, R. Kiernan, R. Benarous,
Benkirane,
S.
Emiliani
Requirement
for
SWI/SNF
Chromatin-Remodeling Complex in Tat-mediated Activation of
143
the HIV-1 Promoter. EMBO J. 25, 690–1699 (2006). doi:
10.1038/sj.emboj.7601074
62.
I. Lemasson, N.J. Polakowski, P.J. Laybourn, J.K. Nyborg.
Tax-dependent
Displacement
of
Nucleosomes
During
Transcriptional Activation of Human T-cell Leukemia Virus
Type
1.
J. Biol. Chem. 281, 3075–3082 (2006). doi:
10.1074/jbc.M512193200
63.
H. Iba, T. Mizutani, T. Ito. SWI/SNF chromatin
remodeling complex and retroviral gene silencing. Rev. Med.
Virol. 13, 99–110 (2003). doi: 10.1002/rmv.378 pmid: 12627393
64.
Kennison JA. The Polycomb and trithorax group proteins
of Drosophila: trans-regulators of homeotic gene function.
Annu
Rev
Genet.
29,
289-303
(1995).
doi:
10.1146/annurev.ge.29.120195.001445 pmid: 8825476
65.
K. Laue, R. S ajshekar, A.J. Courtney, Z.A. Lewis, M.G.
Goll. The maternal to zygotic transition regulates genome-wide
heterochromatin establishment in the zebrafish embryo. Nat.
Commun. 10,551 (2019). doi: 10.1038/s41467-019-09582-3
pmid: 30948728
144
66.
A. Zoch, T. Auchynnikava, R.V. Berrens, Y. Kabayama, T.
Schöpp, M. Heep, L. Vasiliauskaitė, Y.A. Pérez-Rico, A.G. Cook,
A. Shkumatava, J. Rappsilber, R.C. Allshire, D. O'Carroll.
SPOCD1 is an essential executor of piRNA-directed de novo
DNA
methylation.
Nature.
10.1038/s41586-020-2557-5
584,635-639
pmid: 32674113
145
(2020).
doi:
9. Acknowledgement
146
Acknowledgments
At first, I owe my deepest gratitude to Prof. Mikiko C.
Siomi for her guidance and encouragement. Dr. Kaoru Sato and
Dr. Kensaku Murano
give
me
insightful comments
and
suggestions. I thank Dr. Lumi Negishi for performing mass
spectrometry analyses. I also thank Akiko Takahashi, Ken
Ohsumi, Mina Horikoshi and Masaru Ariura for technical
assistance, Dr. Tetsutaro Sumiyoshi, Dr. Yuka W. Iwasaki, Dr.
Shigeki Hirakata and Dr. Hikari Yoshitane for advices on
bioinformatic analyses, Hiromi Yamada for proofreading of the
text and members of the Siomi laboratories. Particularly Prof.
Haruhiko Siomi, Dr. Yuka W. Iwasaki and Dr. Soichiro Yamanaka
gave me constructive comments and warm encouragement. We
also thank Prof. Lei Zhang and Prof. Susumu Hirose for sharing
antibodies and Prof. Katsuhiko Shirahige for advices on ChIP.
147
...